A man in a wheelchair was found dead in a river in the northern city of Hamburg, according to local firefighters.
Witnesses saw him fall into the water and despite a rescue effort that included divers, a boat and a helicopter, he could not be saved.
A pedestrian also died in Hamburg after he was hit by scaffolding that fell from the seventh floor of a building, police said. He was taken to hospital where he later died.
A 53-year-old man was the third person to be killed in the storm after being crushed by a tree in the west German spa town Brilon. The man was working in the forest when a 20-metre (65-foot) tall spruce tree fell on him, local police said.
The storm crossed western and northern Germany on Wednesday and was bound for the east of the country, German meteorologists said.
Several regions of Germany have issued warnings advising residents to stay home while emergency services clear roads and fix power outages.
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